How does ss-DNA recognize the chirality of carbon nanotubes?

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Molecular dynamics simulations are performed to reveal the mechanism of the chiral recognition of single wall carbon nanotubes (SWNTs) by single strand DNA. ss-DNA composed of 10 thymine bases are used for the simulations, as this is known from experiment to have high dispersion ability. Two SWNTs, (10,0) and (8,3), having comparable diameters but different chiralities are examined, with emphasis on identifying the most stable ss-DNA/SWNT structures that arise in explicit water simulations at 300. K. We find that the thymine bases are preferentially stacked on the SWNT surface, with the backbone of the ss-DNA adopting a helical structure. The stacked bases show different π-stacked orientations depending on SWNT chirality, and this induces a chirality-dependent pitch to the ss-DNA even though the SWNT diameters are comparable. This leads to unequal interactions with the stationary phase when eluted in chromatographic experiments, separating the SWNTs according to their chirality.

Original languageEnglish
JournalJournal of Computational Science
Publication statusAccepted/In press - 7 Apr 2015



  • Base orientation
  • Chirality
  • DNA
  • Helix
  • Molecular dynamics simulation
  • Molecular recognition
  • Single wall carbon nanotubes
  • π-π interaction

ASJC Scopus subject areas

  • Computer Science(all)
  • Modelling and Simulation
  • Theoretical Computer Science

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